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Publications citing DeviceEditor
32. Shi, Z., Vickers, C.E. (2016) Molecular Cloning Designer Simulator (MCDS): All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects. Metabolic Engineering Open volume 3, pp. 173 - 186. DOI:dx.doi.org/10.1016/j.meteno.2016.05.003

31. Trinh, C.T., Mendoza, B., 2016. Modular Cell Design for Rapid, Efficient Strain Engineering  towards Industrialization of Biology, Curr Opin Chem Eng, 14:18–25

30. Breitling R, Achcar F, Takano E. (2013) Modeling challenges in the synthetic biology of secondary metabolism. ACS Synth Biol. 2(7):373-8. doi:
10.1021/sb4000228.

29. Cox III, R.S., Koro Nishikata, K., Shimoyama, S., Yoshida, Y., Matsui, M., Makita, Y., and Toyoda, T. (2013) PromoterCAD: data-driven design of plant regulatory DNA.  Nucl. Acids Res. DOI: 10.1093/nar/gkt518  

28. Michal Galdzicki, Kevin P Clancy, Ernst Oberortner, Matthew Pocock, Jacqueline Y Quinn, Cesar A Rodriguez, Nicholas Roehner, Mandy L Wilson, Laura Adam, J Christopher Anderson, Bryan A Bartley, Jacob Beal, Deepak Chandran, Joanna Chen, Douglas Densmore, Drew Endy, Raik Grünberg, Jennifer Hallinan, Nathan J Hillson, Jeffrey D Johnson, Allan Kuchinsky, Matthew Lux, Goksel Misirli, Jean Peccoud, Hector A Plahar, Evren Sirin, Guy-Bart Stan, Alan Villalobos, Anil Wipat, John H Gennari, Chris J Myers, Herbert M Sauro. (2014). The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology 32:545-550.

27. Quin MB, Schmidt-Dannert C. Designer microbes for biosynthesis. (2014) Curr Opin Biotechnol. 2014 Oct;29:55-61. doi: 10.1016/j.copbio.2014.02.014.

26. Qi H, Li BZ, Zhang WQ, Liu D, Yuan YJ. (2015) Modularization of genetic elements promotes synthetic metabolic engineering. Biotechnol Adv. 2015 Nov
15;33(7):1412-9. doi: 10.1016/j.biotechadv.2015.04.002.

25. Linshiz, Jensen, Stawski, Bi, Elsbree, Jiao, Kim, Mathies, Keasling, Hillson. (2016) End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis. Journal of Biological Engineering 10

24. Sadowski, Michael I.; Grant, Chris; Fell, Tim S. (2016) Harnessing QbD, Programming Languages, and Automation for Reproducible Biology. TRENDS IN BIOTECHNOLOGY 34 (3), 214-227.

23. Sarah Rodriguez, Charles M. Denby, T. Van Vu, Edward E. K. Baidoo, George Wang and Jay D. Keasling. (2016) ATP citrate lyase mediated cytosolic acetyl-CoA biosynthesis increases mevalonate production in Saccharomyces cerevisiae. Microbial Cell Factories 201615:48 DOI: 10.1186/s12934-016-0447-1

22. Beck, D. A. C., Carothers, J. M., Subramanian, V. R. and Pfaendtner, J. (2016), Data science: Accelerating innovation and discovery in chemical engineering. AIChE J., 62: 1402–1416. doi:10.1002/aic.15192

21. Nielsen, Jens and Keasling, Jay D. (2016) Engineering Cellular Metabolism. Cell 164, 1185-1197. DOI: http://dx.doi.org/10.1016/j.cell.2016.02.004

20. Steve C. C. Shih, Garima Goyal, Peter W. Kim, Nicolas Koutsoubelis, Jay D. Keasling, Paul D. Adams, Nathan J. Hillson, and Anup K. Singh. (2015) A Versatile Microfluidic Device for Automating Synthetic Biology. ACS Synthetic Biology Article ASAP. DOI:10.1021/acssynbio.5b00062

19.  Oberortner E, Densmore D. (2014) Web-Based Software Tool for Constraint-Based Design  Specification of Synthetic Biological Systems. ACS Synth Biol. DOI: 10.1021/sb500352b

18. Nicholas Roehner, Ernst Oberortner, Matthew Pocock, Jacob Beal, Kevin Clancy, Curtis Madsen, Goksel Misirli, Anil Wipat, Herbert Sauro, and Chris J. Myers. (2014) Proposed Data Model for the Next Version of the Synthetic Biology Open Language. ACS Synthetic Biology. DOI: 10.1021/sb500176h

17. Chris J. Paddon and Jay D. Keasling. (2014) Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nature Reviews Microbiology doi:10.1038/nrmicro3240

16. Nicholas Roehner, and Chris J. Myers. (2014). Directed Acyclic Graph-Based Technology Mapping of Genetic Circuit Models. ACS Synth. Biol. DOI: 10.1021/sb400135t

15. Linshiz, G., Stawski, N., Goyal, G., Bi, C., Poust, S., Sharma, M., Mutalik, V., Keasling, J.D., and Hillson, N.J. (2014). PR-PR: Cross-Platform Laboratory Automation System. ACS Synthetic Biology. DOI: 10.1021/sb4001728

14. Nicholas Roehner and Chris J. Myers (2013). A Methodology to Annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language. ACS Synthetic Biology 3 (2), 57-66. DOI: 10.1021/sb400066m

13. Bi,  C., Su, P., Müller,  J., Yeh, Y.C., Chhabra, S.R., Beller, H.R., Singer, S.W., and Hillson, N.J. (2013) "Development of a broad-host synthetic biology toolbox for ralstonia eutropha and its application to engineering hydrocarbon biofuel production". Microbial Cell Factories 12:107. DOI: 10.1186/1475-2859-12-107

12. Fisher, A.B., Canfield, A.B., Hayward, L.C., Fong, S.S., and McArthur IV, G.H. (2013) "Ex vivo DNA assembly". Front. Bioeng. Biotechnol. DOI: 10.3389/fbioe.2013.00012.

11. Carothers, J. (2013) "Design-driven, multi-use research agendas to enable applied synthetic biology for global health". Syst Synth Biol. DOI 10.1007/s11693-013-9118-2

10. Narjeskhatoon Habibi, Siti Zaiton Mohd Hashim, Cesar A. Rodriguez, Mohd Razip Samian. (2013) "A Review of CADs, Languages and Data Models for Synthetic Biology" Jurnal Teknologi 63 (1): DOI: 10.11113/jt.v63.1644

9. Kahl, L.J., and Endy, D. (2013) A survey of enabling technologies in synthetic biology. Journal of Biological Engineering 7:13 DOI:10.1186/1754-1611-7-13.

8. Bhatia, S., and Densmore, D. (2013) Pigeon: a design visualizer for synthetic biology. ACS Synthetic Biology. DOI: 10.1021/sb400024s

7. Linshiz, G., Goldberg, A., Konry, T., and Hillson, N.J. (2013) The Fusion of Biology, Computer Science, and Engineering – towards efficient and successful synthetic biology. Perspectives in Biology and Medicine 55 (4), 503-520. DOI: 10.1353/pbm.2012.0044

6. Linshiz, G., Stawski, N., Poust, S., Bi, C., Keasling, J.D., and Hillson, N.J. (2012). PaR-PaR Laboratory Automation platform. ACS Synthetic Biology. DOI: 10.1021/sb300075t

5. Jacob Beal, Ron Weiss, Douglas Densmore, Aaron Adler, Evan Appleton, Jonathan Babb, Swapnil Bhatia, Noah Davidsohn, Traci Haddock, Joseph Loyall, Richard Schantz, Viktor Vasilev, and Fusun Yaman. (2012) An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications. ACS Synthetic Biology. Just Accepted Manuscript. DOI: 10.1021/sb300030d

4. Yaman F, Bhatia S, Adler A, Densmore D, and Beal J. (2012) Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks. ACS Synthetic Biology. Just Accepted Manuscript. DOI: 10.1021/sb300032y.

3. Wu K, Rao CV. (2012) Computational methods in synthetic biology: towards computer-aided part design. Curr Opin Chem Biol. DOI: 10.1016/j.cbpa.2012.05.003 PubMed PMID: 22727029.

2. Kitney R, Freemont P. (2012) Synthetic biology - the state of play. FEBS Lett. DOI: 10.1016/j.febslet.2012.06.002 PubMed PMID: 22704968.

1. Galdzicki M,  Chandran D, Jennari JH, and Sauro HM. (2011) "Data Model Standardization for Synthetic Biomolecular Circuits and Systems" in Design and Analysis of Bio-molecular Circuits, Koeppl H., Densmore, D., di Bernardo, M., and Setti, G. (Editors), Springer-Verlag, 1st Edition, 281-293.